Format for Individual Target pages (copy this list to new Target page and then fill in for your target):
*Target (protein/gene name): Viral neuraminidase *NCBI Gene # or RefSeq#: NC_001422 *Protein ID (NP or XP #) or Wolbachia#: *Organism (including strain): Orthomyxoviridae: Influenzavirus A Etiologic Risk Group (see link below): */Disease Information (sort of like the Intro to your Mini Research Write up):
The flu, also called Influenza, is an infectious disease which is instigated by the influenza virus. Influenza is most commonly experienced with a high fever, runny nose, sore throat, and feeling exhausted. Symptoms typically last than a week and are usually experienced two days after being exposed to the virus. There are three strains of the virus: Type A, Type B, and Type C and all are usually spread though the air. There is typically a global annual outbreak of Influenza, which results in a quarter million to half a million deaths. Viral neuraminidase is an enzyme located on the virus' surface and plays an essential role in the organism virulence. It allows the virus to be released from the host cell and pass on to infect other organisms. Viral neuraminidase work by removing the sialic acid group from a glycoprotein and are also essential for the rapid replication of the influenza virus.
Link to TDR Targets page (if present): N/A Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.) https://www.ncbi.nlm.nih.gov/gene/2546398 Essentiality of this protein: required for host cell to infect other organisms
Is it a monomer or multimer as biological unit? (make prediction athttp://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): multimer Complex of proteins?: Yes Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):
Viral neuraminidase has been marked as a promising target but has yet been used to make an effective drug. Ulrike Grienke; Michaela Schmidtke; Grafenstein, S.; Johannes Kirchmair; R. Liedl, K.; M. Rollinger, J. Influenza neuraminidase: A druggable target for natural products http://pubs.rsc.org/en/content/articlehtml/2012/np/c1np00053e (accessed May 5, 2018)
*EC#: Link to BRENDA EC# page: -- Show screenshot of BRENDA enzyme mechanism schematic
Image result for BRENDA enzyme mechanism schematic viral neuraminidase
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-cell culture-based assays
-in vitro assays with bacterial NA, like C. perfringens and V. cholerae, to pinpoint anti0viral agents using fluorescence and chemiiluminescence based testing systems that work with viral and bacterial NA
Structure (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model: 7NN9
-- For Homology Model option: N/A
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB N/A
---- Query Coverage: N/A
---- Max % Identities: N/A
---- % Positives N/A
---- Chain used for homology: N/A
Current Inhibitors: zanamivir, oseltamivir, peramivir
Expression Information (has it been expressed in bacterial cells): yes Purification Method: Image of protein (PyMol with features delineated and shown separately): *Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
*length of your protein in Amino Acids 469 Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website 45.55 kDa Molar Extinction coefficient of your protein at 280 nm wavelength: 12.6 l/mol*cm TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. *CDS Gene Sequence (paste as text only):
*GC% Content for gene: 61% *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): N/A *GC% Content for gene (codon optimized): N/A
Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
**
Format for Individual Target pages (copy this list to new Target page and then fill in for your target):
*Target (protein/gene name): Viral neuraminidase*NCBI Gene # or RefSeq#: NC_001422
*Protein ID (NP or XP #) or Wolbachia#:
*Organism (including strain): Orthomyxoviridae: Influenzavirus A
Etiologic Risk Group (see link below):
*/Disease Information (sort of like the Intro to your Mini Research Write up):
The flu, also called Influenza, is an infectious disease which is instigated by the influenza virus. Influenza is most commonly experienced with a high fever, runny nose, sore throat, and feeling exhausted. Symptoms typically last than a week and are usually experienced two days after being exposed to the virus. There are three strains of the virus: Type A, Type B, and Type C and all are usually spread though the air. There is typically a global annual outbreak of Influenza, which results in a quarter million to half a million deaths. Viral neuraminidase is an enzyme located on the virus' surface and plays an essential role in the organism virulence. It allows the virus to be released from the host cell and pass on to infect other organisms. Viral neuraminidase work by removing the sialic acid group from a glycoprotein and are also essential for the rapid replication of the influenza virus.
Link to TDR Targets page (if present): N/A
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)
https://www.ncbi.nlm.nih.gov/gene/2546398
Essentiality of this protein: required for host cell to infect other organisms
Is it a monomer or multimer as biological unit? (make prediction at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): multimer
Complex of proteins?: Yes
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):
Viral neuraminidase has been marked as a promising target but has yet been used to make an effective drug.
Ulrike Grienke; Michaela Schmidtke; Grafenstein, S.; Johannes Kirchmair; R. Liedl, K.; M. Rollinger, J. Influenza neuraminidase: A druggable target for natural products http://pubs.rsc.org/en/content/articlehtml/2012/np/c1np00053e (accessed May 5, 2018)
*EC#:
Link to BRENDA EC# page:
-- Show screenshot of BRENDA enzyme mechanism schematic
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-cell culture-based assays
-in vitro assays with bacterial NA, like C. perfringens and V. cholerae, to pinpoint anti0viral agents using fluorescence and chemiiluminescence based testing systems that work with viral and bacterial NA
-- link to Sigma (or other company) page for assay (see Sigma links below)
-- -or link (or citation) to paper that contains assay information
http://pubs.rsc.org/en/content/articlehtml/2012/np/c1np00053e
-- links to assay reagents (substrates) pages.
https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/General_Information/2/biofiles_issue10.pdf
--- List cost and quantity of substrate reagents, supplier, and catalog #
N/A because unspecified volume, Sigma-Aldrich
Structure (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model: 7NN9
-- For Homology Model option: N/A
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB N/A
---- Query Coverage: N/A
---- Max % Identities: N/A
---- % Positives N/A
---- Chain used for homology: N/A
Current Inhibitors: zanamivir, oseltamivir, peramivir
Expression Information (has it been expressed in bacterial cells): yes
Purification Method:
Image of protein (PyMol with features delineated and shown separately):
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
*length of your protein in Amino Acids 469
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website 45.55 kDa
Molar Extinction coefficient of your protein at 280 nm wavelength: 12.6 l/mol*cm
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
<span style="background-color: #ffffff; font-family: monospace,serif;"><span class="feature"> MVRSYYPSECHADYFDFERIEALKPAIEACGISTLSQSPMLGFH KQMDNRIKLLEEILSFRMQGVEFDNGDMYVDGHKAASDVRDEFVSVTEKLMDELAQCY NVLPQLDINNTIDHRPEGDEKWFLENEKTVTQFCRKLAAERPLKDIRDEYNYPKKKGI KDECSRLLEASTMKSRRGFAIQRLMNAMRQAHADGWFIVFDTLTLADDRLEAFYDNPN ALRDYFRDIGRMVLAAEGRKANDSHADCYQYFCVPEYGTANGRLHFHAVHFMRTLPTG SVDPNFGRRVRNRRQLNSLQNTWPYGYSMPIAVRYTQDAFSRSGWLWPVDAKGEPLKA TSYMAVGFYVAKYVNKKSDMDLAAKGLGAKEWNNSLKTKLSLLPKKLFRIRMSRNFGM KMLTMTNLSTECLIQLTKLGYDATPFNQILKQNAKREMRLRLGKVTVADVLAAQPVTT NLLKFMRASIKMIGVSNLQSFIASMTQKLTLSDISDESKNYLDKAGITTACLRIKSKW TAGGK"</span></span>*GC% Content for gene: 61%*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): N/A
*GC% Content for gene (codon optimized): N/A
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
**